📄 Category

systems biology

121 papers

Systems biology moves beyond studying individual genes or proteins to understand how they work together as a complex, living network. Instead of looking at isolated parts, this field examines the intricate conversations between molecules that drive life, revealing how cellular systems respond to changes and maintain balance. It is a holistic approach that turns vast amounts of data into a coherent story of how organisms function as a whole.

At Gist.Science, we ensure these breakthroughs remain accessible to everyone by processing every new preprint in this category directly from bioRxiv. Our team generates both plain-language explanations for the curious mind and detailed technical summaries for researchers, bridging the gap between rapid scientific discovery and clear understanding.

Below are the latest preprints in systems biology, freshly curated and summarized to help you navigate the cutting edge of network science.

📄 systems biology

Deep Mechanistic Models reveal pathway-extrinsic drivers of mammary MAPK signalling heterogeneity

This paper introduces Deep Mechanistic Models (DMMs), a framework that integrates semi-supervised representation learning with ordinary differential equation models to reveal that mammary MAPK signalling heterogeneity is primarily driven by pathway-extrinsic factors rather than core pathway variations, while simultaneously using model discrepancies to identify novel biological mechanisms.

Fabrini, G., Froehlich, F.2026-07-31
📄 systems biology

Covariant Biochemical Systems Theory: cBST1~cBST3 Descriptors and Quantitative Validation

This paper introduces a covariant hierarchy of descriptors (cBST1–cBST3) for Biochemical Systems Theory that ensures coordinate consistency under nonlinear reparameterizations and demonstrates through quantitative validation on yeast glycolysis models that these higher-order terms significantly reduce approximation errors and accurately predict truncation behavior compared to classical methods.

Oosawa, C.2026-07-29
📄 systems biology

Structural characterization of stochastic detailed balance in chemical reaction networks

This paper systematically characterizes the volume dependence of stochastic detailed balance in chemical reaction networks by introducing a four-type classification, distinguishing between parameter-dependent and structurally enforced balance, and identifying network classes that satisfy detailed balance for all volumes and rate constants while enabling the construction of systems with double-well global potentials.

Ma, S., Li, Y.2026-07-28
📄 systems biology

Proteome-wide QTL mapping enables gene-protein-phenotype metabolic network construction in a genetically diverse MASLD mouse model

By integrating deep proteomic profiling with QTL mapping in a genetically diverse mouse model of MASLD, this study constructs a comprehensive gene-protein-phenotype network that identifies the E3 ubiquitin ligase Ubr1 as a central regulator linking proteostasis and lipid metabolism to disease susceptibility.

Robinson, M. L., Benegiamo, G., Liu, W., Williams, M. T., Smith, G. I., Klein, S., Auwerx, J., Coon, J. J.2026-07-28
📄 systems biology

Unlocking substrate specificities of human solute carrier proteins using untargeted metabolomics

This study introduces a scalable, untargeted metabolomics platform using Xenopus oocytes incubated in human serum to successfully deorphanize and characterize the substrate specificities of five human solute carrier proteins, recovering known substrates and identifying novel transported metabolites.

Zhang, Y., Stanchev, L. D., Schulz, F. C., Rago, D., Acevedo-Rocha, C. G., Santos Delgado, A., Kell, D. B., Borodina, I.2026-07-28
📄 systems biology

Interplay between store-operated calcium entry and mitochondrial phosphate handling modulates force and fatigue during exercise

This study employs a quantitative biophysical model to demonstrate that store-operated calcium entry (SOCE) enhances skeletal muscle force during resistance exercise by sustaining calcium release, but can exacerbate fatigue during high-intensity training due to phosphate accumulation, a trade-off that is modulated by mitochondrial phosphate uptake.

Francis, E. A., Hamid, J., Kumar, A., Rangamani, P.2026-07-24
📄 systems biology

Quantitative Description of C. elegans mRNA Landscapes From High Coverage Single Cell Transcriptomes

This study introduces a novel supervised clustering approach for high-coverage single-cell RNA sequencing data to quantitatively characterize *C. elegans* mRNA landscapes, revealing unprecedented cell-type-specific gene expression programs and identifying novel tissue-restricted genes that were previously undetectable at lower coverage thresholds.

Bernard, F., Kandel, E., Dargere, D., Cornes, E., Dupuy, D.2026-07-21
📄 systems biology

ChatGEM: An Agentic Architecture Enabling Interactive Simulation of Genome-Scale Metabolic Models

This paper introduces ChatGEM, an agentic platform that leverages natural language and retrieval-augmented generation to democratize genome-scale metabolic modeling, enabling researchers without computational expertise to perform complex simulations and successfully identify optimal microbial strains for bioproduction.

Chowdhury, N., George, A., Purohit, S., Contolesi, A., Bredeweg, E. L., Czajka, J., Stratton, K. G., Gao, Y., Stephenson (…)2026-07-21
📄 systems biology

Kinome-wide CRISPR/Cas9-knockout screening reveals critical protein kinases in vasopressin V2-receptor signaling

This study employs a kinome-wide CRISPR/Cas9 knockout screen in a vasopressin V2-receptor signaling model to identify critical positive and negative protein kinase regulators, revealing known players like PKA and novel factors such as Dyrk1a and Stk11/LKB1 that modulate AQP2 expression through distinct mechanisms involving cell differentiation and CRTC protein regulation.

Park, E., Chen, L., Raghuram, V., Khan, S., Murillo-de-Ozores, A. R., Chou, C.-L., Yang, C.-R., Knepper, M. A.2026-07-10